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Long non-coding mRNA

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https://www.readbyqxmd.com/read/28081465/biological-function-and-mechanism-of-lncrna-meg3-in-tenon-s-capsule-fibroblasts-proliferation-by-meg3-nrf2-protein-interaction
#1
Yuan Wang, Jing Wang, Li-Juan Wei, Dong-Mei Zhu, Jin-Song Zhang
OBJECTIVE: The proliferation of Tenon's capsule fibroblasts after glaucoma filtration surgery is a harmful element for operation failure. However, the underlying mechanism remains unclear. In this study, we evaluated the role of long non-coding RNA (lncRNA)-MEG3 in the proliferation of Glaucoma Tenon's capsule fibroblasts (GTFs) with a model of transforming growth factor-β (TGF-β)-induced proliferation which has been used in previous studies to explore the mechanism underlying glaucoma surgery failure...
January 9, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/28062751/transcriptome-wide-mapping-of-rna-5-methylcytosine-in-arabidopsis-mrnas-and-non-coding-rnas
#2
Rakesh David, Alice Burgess, Brian Parker, Jun Li, Kalinya Pulsford, Tennille Sibbritt, Thomas Preiss, Iain R Searle
Post-transcriptional methylation of RNA cytosine residues to 5-methylcytosine (m5C) is an important modification with diverse roles, such as regulating stress responses, stem cell proliferation, and RNA metabolism. Here, we used RNA bisulfite sequencing (bsRNA-seq) for transcriptome-wide quantitative mapping of m5C in the model plant, Arabidopsis thaliana. We discovered more than a thousand m5C sites in Arabidopsis mRNAs, long non-coding RNAs, and other non-coding RNAs across three tissue types (siliques, seedling shoots, and roots) and validated a number of these sites...
January 6, 2017: Plant Cell
https://www.readbyqxmd.com/read/28057128/-expression-and-function-of-long-intergenic-non-protein-coding-rna-regulator-of-reprogramming-in-high-grade-ovarian-serous-cancer
#3
H H Jiang, Y H Lou, X Y Wang, Y Han, Z M Cui
Objective: To investigate the expression of long intergenic non-protein coding RNA-regulator of reprogramming (Linc-ROR) in high-grade ovarian serous cancer, and explore the relationship between Linc-ROR expression and biological function of high-grade ovarian serous cancer. Methods: A total of 34 high-grade ovarian serous cancer tissue samples and 19 normal fallopian tube tissue samples were collected between June 2014 and February 2016. Real-time reverse transcription (RT)-PCR was used to detect the Linc-ROR mRNA expression in different samples...
December 25, 2016: Zhonghua Fu Chan Ke za Zhi
https://www.readbyqxmd.com/read/28053114/feelnc-a-tool-for-long-non-coding-rna-annotation-and-its-application-to-the-dog-transcriptome
#4
Valentin Wucher, Fabrice Legeai, Benoît Hédan, Guillaume Rizk, Lætitia Lagoutte, Tosso Leeb, Vidhya Jagannathan, Edouard Cadieu, Audrey David, Hannes Lohi, Susanna Cirera, Merete Fredholm, Nadine Botherel, Peter A J Leegwater, Céline Le Béguec, Hille Fieten, Jeremy Johnson, Jessica Alföldi, Catherine André, Kerstin Lindblad-Toh, Christophe Hitte, Thomas Derrien
Whole transcriptome sequencing (RNA-seq) has become a standard for cataloguing and monitoring RNA populations. One of the main bottlenecks, however, is to correctly identify the different classes of RNAs among the plethora of reconstructed transcripts, particularly those that will be translated (mRNAs) from the class of long non-coding RNAs (lncRNAs). Here, we present FEELnc (FlExible Extraction of LncRNAs), an alignment-free program that accurately annotates lncRNAs based on a Random Forest model trained with general features such as multi k-mer frequencies and relaxed open reading frames...
January 3, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28043146/microarray-analysis-of-long-non-coding-rnas-related-to-microrna-148b-in-gastric-cancer
#5
Y Song, J Sun, Y Xu, J Liu, P Gao, X Chen, J Zhao, Z Wang
The miR-148/152 family (miR-148a, miR-148b, miR-152) is differentially expressed in gastric cancer tissues and non-tumor tissues. Our previous studies indicated that miR-148/152 family is important in the tumorigenesis and development of gastric cancer. We also found several target genes that were regulated by the miR-148/152 family and several factors that could influence members of this family. However, the molecular mechanisms and function of this family in gastric cancer remain unclear. Recently, long non-coding RNAs (lncRNAs) have been found to play an important role in the pathogenesis of many diseases...
January 3, 2017: Neoplasma
https://www.readbyqxmd.com/read/28035067/long-non-coding-rna-ak058003-as-a-precursor-of-mir-15a-interacts-with-hur-to-inhibit-the-expression-of-%C3%AE-synuclein-in-hepatocellular-carcinoma-cells
#6
Xiaoqin He, Yongfa Zheng, Yuefeng Zhang, Yuanyuan Gan, Yujie Zhou, Huilin Liang, Dongcheng Wu, Wei Ge, Junjian Deng, Ximing Xu
Long non-coding RNAs (lncRNAs) have been identified as critical players in multiple cancers and lncRNAs are tightly linked to cancer progression. However, only little amount of lncRNAs have been identified to participate in the molecular mechanisms of the progression of hepatocellular carcinoma. In this study, we found that lncRNA-AK058003 is down-regulated in hepatocellular carcinoma tissues and it is associated with the relapse and metastasis of the cancer. Furthermore, lncRNA-AK058003 acts as a tumor suppressor, suppressing hepatocellular carcinoma cell proliferation and metastasis in vitro and in vivo...
December 27, 2016: Oncotarget
https://www.readbyqxmd.com/read/28033318/a-point-mutation-in-a-lincrna-upstream-of-gdnf-is-associated-to-a-canine-insensitivity-to-pain-a-spontaneous-model-for-human-sensory-neuropathies
#7
Jocelyn Plassais, Laetitia Lagoutte, Solenne Correard, Manon Paradis, Eric Guaguère, Benoit Hédan, Alix Pommier, Nadine Botherel, Marie-Christine Cadiergues, Philippe Pilorge, David Silversides, Maud Bizot, Mark Samuels, Carme Arnan, Rory Johnson, Christophe Hitte, Gilles Salbert, Agnès Méreau, Pascale Quignon, Thomas Derrien, Catherine André
Human Hereditary Sensory Autonomic Neuropathies (HSANs) are characterized by insensitivity to pain, sometimes combined with self-mutilation. Strikingly, several sporting dog breeds are particularly affected by such neuropathies. Clinical signs appear in young puppies and consist of acral analgesia, with or without sudden intense licking, biting and severe self-mutilation of the feet, whereas proprioception, motor abilities and spinal reflexes remain intact. Through a Genome Wide Association Study (GWAS) with 24 affected and 30 unaffected sporting dogs using the Canine HD 170K SNP array (Illumina), we identified a 1...
December 2016: PLoS Genetics
https://www.readbyqxmd.com/read/28008089/extracellular-vesicles-their-role-in-cancer-biology-and-epithelial-mesenchymal-transition
#8
REVIEW
Shashi K Gopal, David W Greening, Alin Rai, Maoshan Chen, Rong Xu, Adnan Shafiq, Rommel A Mathias, Hong-Jian Zhu, Richard J Simpson
Cell-cell communication is critical across an assortment of physiological and pathological processes. Extracellular vesicles (EVs) represent an integral facet of intercellular communication largely through the transfer of functional cargo such as proteins, messenger RNAs (mRNAs), microRNA (miRNAs), DNAs and lipids. EVs, especially exosomes and shed microvesicles, represent an important delivery medium in the tumour micro-environment through the reciprocal dissemination of signals between cancer and resident stromal cells to facilitate tumorigenesis and metastasis...
January 1, 2017: Biochemical Journal
https://www.readbyqxmd.com/read/28004750/snhg5-promotes-colorectal-cancer-cell-survival-by-counteracting-stau1-mediated-mrna-destabilization
#9
Nkerorema Djodji Damas, Michela Marcatti, Christophe Côme, Lise Lotte Christensen, Morten Muhlig Nielsen, Roland Baumgartner, Helene Maria Gylling, Giulia Maglieri, Carsten Friis Rundsten, Stefan E Seemann, Nicolas Rapin, Simon Thézenas, Søren Vang, Torben Ørntoft, Claus Lindbjerg Andersen, Jakob Skou Pedersen, Anders H Lund
We currently have limited knowledge of the involvement of long non-coding RNAs (lncRNAs) in normal cellular processes and pathologies. Here, we identify and characterize SNHG5 as a stable cytoplasmic lncRNA with up-regulated expression in colorectal cancer. Depletion of SNHG5 induces cell cycle arrest and apoptosis in vitro and limits tumour outgrowth in vivo, whereas SNHG5 overexpression counteracts oxaliplatin-induced apoptosis. Using an unbiased approach, we identify 121 transcript sites interacting with SNHG5 in the cytoplasm...
December 22, 2016: Nature Communications
https://www.readbyqxmd.com/read/27991686/co-expression-changes-of-lncrnas-and-mrnas-in-the-cervical-sympathetic-ganglia-in-diabetic-cardiac-autonomic-neuropathic-rats
#10
Guilin Li, Xuan Sheng, Yurong Xu, Huaide Jiang, Chaoran Zheng, Jingjing Guo, Shanshan Sun, Zhihua Yi, Shulan Qin, Shuangmei Liu, Yun Gao, Chunping Zhang, Hong Xu, Bing Wu, Lifang Zou, Shangdong Liang, Gaochun Zhu
Cardiac autonomic neuropathy in Type 2 diabetes (T2D) is often a devastating complication. Long non-coding RNAs (lncRNAs) have important effects on both normal development and disease pathogenesis. In this study, we explored the expression profiles of some lncRNAs involved in inflammation which may be co-expressed with messenger RNA (mRNA) in superior cervical and stellate ganglia after type 2 diabetic injuries. Total RNA isolated from 10 pairs of superior cervical and stellate ganglia in diabetic and normal male rats was hybridized to lncRNA arrays for detections...
December 19, 2016: Journal of Neuroscience Research
https://www.readbyqxmd.com/read/27974853/human-cellular-cyba-utr-sequences-increase-mrna-translation-without-affecting-the-half-life-of-recombinant-rna-transcripts
#11
Mehrije Ferizi, Manish K Aneja, Elizabeth R Balmayor, Zohreh Sadat Badieyan, Olga Mykhaylyk, Carsten Rudolph, Christian Plank
Modified nucleotide chemistries that increase the half-life (T1/2) of transfected recombinant mRNA and the use of non-native 5'- and 3'-untranslated region (UTR) sequences that enhance protein translation are advancing the prospects of transcript therapy. To this end, a set of UTR sequences that are present in mRNAs with long cellular T1/2 were synthesized and cloned as five different recombinant sequence set combinations as upstream 5'-UTR and/or downstream 3'-UTR regions flanking a reporter gene. Initial screening in two different cell systems in vitro revealed that cytochrome b-245 alpha chain (CYBA) combinations performed the best among all other UTR combinations and were characterized in detail...
December 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27974506/ionizing-radiation-regulates-long-non-coding-rnas-in-human-peripheral-blood-mononuclear-cells
#12
Lucian Beer, Lucas Nemec, Tanja Wagner, Robin Ristl, Lukas M Altenburger, Hendrik Jan Ankersmit, Michael Mildner
Long non-coding RNAs (lncRNAs) are non-protein coding transcripts that modulate mRNA and microRNA (miRNA) expression, thereby controlling multiple cellular processes, including transcriptional regulation of gene expression, cell differentiation and apoptosis. Ionizing radiation (IR), a strong cellular stressor, is known to influence gene expression of irradiated cells, mainly by activation of oxidative processes. Whether and how IR also affects lncRNA expression in human peripheral blood mononuclear cells (PBMCs) is still poorly understood...
December 14, 2016: Journal of Radiation Research
https://www.readbyqxmd.com/read/27966078/analysis-of-pirna-like-small-non-coding-rnas-present-in-axons-of-adult-sensory-neurons
#13
Monichan Phay, Hak Hee Kim, Soonmoon Yoo
Small non-coding RNAs (sncRNAs) have been shown to play pivotal roles in spatiotemporal-specific gene regulation that is linked to many different biological functions. PIWI-interacting RNAs (piRNAs), typically 25-34-nucleotide long, are originally identified and thought to be restricted in germline cells. However, recent studies suggest that piRNAs associate with neuronal PIWI proteins, contributing to neuronal development and function. Here, we identify a cohort of piRNA-like sncRNAs (piLRNAs) in rat sciatic nerve axoplasm and directly contrast temporal changes of piLRNA levels in the nerve following injury, as compared with those in an uninjured nerve using deep sequencing...
December 13, 2016: Molecular Neurobiology
https://www.readbyqxmd.com/read/27965463/ameloblastoma-rna-profiling-uncovers-a-distinct-non-coding-rna-signature
#14
Haleh Davanian, Anangi Balasiddaiah, Robert Heymann, Magnus Sundström, Poppy Redenström, Mikael Silfverberg, David Brodin, Matti Sällberg, Sven Lindskog, Carina Kruger Weiner, Margaret Chen
Ameloblastoma of the jaws remains the top difficult to treat odontogenic tumour and has a high recurrence rate. New evidence suggests that non-coding RNAs (ncRNAs) play a critical role in tumourgenesis and prognosis of cancer. However, ameloblastoma ncRNA expression data is lacking. Here we present the first report of ameloblastoma ncRNA signatures. A total of 95 ameloblastoma cases and a global array transcriptome technology covering > 285.000 full-length transcripts were used in this two-step analysis...
December 10, 2016: Oncotarget
https://www.readbyqxmd.com/read/27942838/deciphering-the-regulation-of-porcine-genes-influencing-growth-fatness-and-yield-related-traits-through-genetical-genomics
#15
Angel M Martínez-Montes, Anixa Muiños-Bühl, Almudena Fernández, Josep M Folch, Noelia Ibáñez-Escriche, Ana I Fernández
Genetical genomics approaches aim at identifying quantitative trait loci for molecular traits, also known as intermediate phenotypes, such as gene expression, that could link variation in genetic information to physiological traits. In the current study, an expression GWAS has been carried out on an experimental Iberian × Landrace backcross in order to identify the genomic regions regulating the gene expression of those genes whose expression is correlated with growth, fat deposition, and premium cut yield measures in pig...
December 10, 2016: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/27936097/petmbase-a-database-of-plant-endogenous-target-mimics-etms
#16
Gökhan Karakülah, Kuaybe Yücebilgili Kurtoğlu, Turgay Unver
MicroRNAs (miRNA) are small endogenous RNA molecules, which regulate target gene expression at post-transcriptional level. Besides, miRNA activity can be controlled by a newly discovered regulatory mechanism called endogenous target mimicry (eTM). In target mimicry, eTMs bind to the corresponding miRNAs to block the binding of specific transcript leading to increase mRNA expression. Thus, miRNA-eTM-target-mRNA regulation modules involving a wide range of biological processes; an increasing need for a comprehensive eTM database arose...
2016: PloS One
https://www.readbyqxmd.com/read/27932875/screening-of-long-non-coding-rna-and-tug1-inhibits-proliferation-with-tgf-%C3%AE-induction-in-patients-with-copd
#17
Wenxiang Tang, Zhenyu Shen, Jiang Guo, Shenghua Sun
OBJECTIVE: To evaluate differentially expressed long noncoding RNAs (lncRNAs) and the potential role of lncRNA TUG1 in patients with chronic obstructive pulmonary disease (COPD). METHODS: Total RNA was extracted from both COPD and non-COPD lung tissues, and microarray analysis was performed with 25,628 lncRNA probes and 20,106 mRNA probes. In addition, five up-regulated and five down-regulated lncRNAs were selected for identification using quantitative real-time polymerase chain reaction...
2016: International Journal of Chronic Obstructive Pulmonary Disease
https://www.readbyqxmd.com/read/27930710/urb-rip-an-adaptable-and-efficient-approach-for-immunoprecipitation-of-rnas-and-associated-rnas-proteins
#18
Kyle A Cottrell, Sergej Djuranovic
Post-transcriptional regulation of gene expression is an important process that is mediated by interactions between mRNAs and RNA binding proteins (RBP), non-coding RNAs (ncRNA) or ribonucleoproteins (RNP). Key to the study of post-transcriptional regulation of mRNAs and the function of ncRNAs such as long non-coding RNAs (lncRNAs) is an understanding of what factors are interacting with these transcripts. While several techniques exist for the enrichment of a transcript whether it is an mRNA or an ncRNA, many of these techniques are cumbersome or limited in their application...
2016: PloS One
https://www.readbyqxmd.com/read/27904771/tumor-suppressive-function-of-long-noncoding-rna-malat1-in-glioma-cells-by-suppressing-mir-155-expression-and-activating-fbxw7-function
#19
Shuanzhu Cao, Yanzhou Wang, Jinquan Li, Mingliang Lv, Haitao Niu, Yong Tian
The human metastasis associated lung adenocarcinoma transcript 1 (MALAT1) is a long non-coding RNA associated with metastasis, and is a favorable prognostic factor for lung cancer. Recent studies have shown that MALAT1 plays an important role in many malignancies. However, little is known about the role of MALAT1 in glioma. In this study, we determined the expression of MALAT1 and explored its prognostic value in glioma. Further, we investigated the regulatory mechanism of MALAT1 in glioma progression. Our results showed that the expression of MALAT1 was significantly decreased in glioma specimens than in noncancerous brain tissues...
2016: American Journal of Cancer Research
https://www.readbyqxmd.com/read/27904675/expression-of-long-non-coding-rna-hotair-in-oral-squamous-cell-carcinoma-tca8113-cells-and-its-associated-biological-behavior
#20
Huawei Liu, Zhiyong Li, Chao Wang, Lin Feng, Haitao Huang, Changkui Liu, Fengxia Li
As a long noncoding RNA, HOX transcript antisense intergenic RNA (HOTAIR) is highly expressed in many types of tumors. However, its expression and function in oral squamous cell carcinoma (OSCC) cells and tissues remains largely unknown. We herein studied the biological functions of HOTAIR in OSCC Tca8113 cells. Real-time quantitative PCR showed that HOTAIR, p21 and p53 mRNA expressions in doxorubicin (DOX)-treated or γ-ray-irradiated Tca8113 cells were up-regulated. Knockdown of p53 expression inhibited DOX-induced HOTAIR up-regulation, suggesting that DNA damage-induced HOTAIR expression may be associated with p53...
2016: American Journal of Translational Research
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